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Open Access Publications from the University of California

Scholarly Works (3 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2016)

Fast photochemical processes are central to a number of problems challenging chemists today. Such problems include atmospheric air pollution driven by solar radiation, development of photocatalysts for clean energy sources and photodynamic therapies for treatment of diseases such as cancer, and light-driven biological phenomena such as vision and vitamin D photosynthesis. Continued improvement of computational methods which can describe and predict such photochemical processes is thus essential. Accordingly, this thesis focuses on two main topics: 1) The development of a spin-symmetry breaking algorithm which for the first time enables homolytic bond cleavage in 'on the fly' density functional non-adiabatic molecular dynamics simulations, and 2) a benchmarking application of the spin-symmetry breaking algorithm to acetaldehyde photochemistry.

Following a brief overview of the challenges inherent within this work, chapter 2 introduces fast photochemical processes and the theoretical foundations of ab inito non-adiabatic molecular dynamics methods. In Chapter 3, a new algorithm for breaking spin-symmetry within linear response time-dependent density functional theory is derived and implemented in the quantum-chemical software suite TURBOMOLE. H2 is used to illustrate the key features of the algorithm, which are: 1) Stability analysis is used to identify critical points on the PES, 2) tight convergence thresholds are used only near triplet instabilities, and 3) adaptive time stepping in the vicinity of triplet instabilities is employed to conserve total energy.

An application of the spin-symmetry breaking algorithm to acetaldehyde photochemistry is then discussed in Chapter 4. Ensembles of approximately 400 trajectories in the ground state and 400 trajectories initialized in the excited state are simulated. Compared to experiment, the spin-symmetry breaking algorithm yields qualitative accuracy for computed branching ratios and total kinetic energy probability distributions. Additionally, two dissociation mechanisms are identified and discussed: The non-transition state theory, ``roaming'', mechanism and new triple-fragmentation mechanisms. Finally, the spin-symmetry breaking algorithm reveals that an improved description of acetaldehyde photodissociation mechanisms may require inclusion of excited state dynamics.

    Cover page: Development and Application of a Spin-symmetry Breaking Algorithm for Ab Initio Non-adiabatic Molecular Dynamics Simulations
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2019)
    Single-cell technologies have described heterogeneity across tissues, but the spatial distribution and forces that drive single-cell phenotypes have not been well defined. Combining single-cell RNA and protein analytics in studying the role of stromal cancer-associated fibroblasts (CAFs) in modulating heterogeneity in pancreatic cancer (pancreatic ductal adenocarcinoma [PDAC]) model systems, we have identified significant single-cell population shifts toward invasive epithelial-to-mesenchymal transition (EMT) and proliferative (PRO) phenotypes linked with mitogen-activated protein kinase (MAPK) and signal transducer and activator of transcription 3 (STAT3) signaling. Using high-content digital imaging of RNA in situ hybridization in 195 PDAC tumors, we quantified these EMT and PRO subpopulations in 319,626 individual cancer cells that can be classified within the context of distinct tumor gland "units." Tumor gland typing provided an additional layer of intratumoral heterogeneity that was associated with differences in stromal abundance and clinical outcomes. This demonstrates the impact of the stroma in shaping tumor architecture by altering inherent patterns of tumor glands in human PDAC.
      Cover page: Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2018)
      QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.
        Cover page: QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids
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